I do not know if this was addressed already but i am using a slightly lesser revision. I am using 5622. Every time I would uncheck the frame limiter by F4 quite often it would lag the emulator itself (not the game) and sometimes take a while for it to get back to normal. For the first time it actually crashed on me. I never had issues in previous versions/revisions.

if it takes a while to recover after disabling the frame limiter, my initial thoughts are your CPU is overheating. The crashing would kind of reaffirm that there is a hardware issue at fault, the enabling and disabling the frame limiter doesnt really do anything drastic, it just stops it sleeping so much every frame, so the emulator is actually doing much less with it off.